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SHES2201 Lecture 4 - Levels of Bioinformatics
SHES2201 Lecture 4 - Levels of Bioinformatics
SHES2201 Lecture 4 - Levels of Bioinformatics
• Class membership
– e.g., predictive toxicology
• Prediction of sequences
– e.g., sequences of protein sub-structures
• Classification hierarchies
– e.g., folds, families, super-families
• Shape descriptions
– e.g., binding site descriptions
• Temporal models
– e.g., activity of cells, metabolic pathways
Bioinformatics Tools
Organism level
Cellular level
Cytomics
Molecular level
Proteomics
Sequence level
Genomics
Levels of biological organization
Organism level
Cytomics
Cellular level
Proteomics
Molecular level
Genomics
Sequence level
Levels of biological organization
Ecology
Species level
Biodiversity
Organism level
Cytomics
Cellular level
Proteomics
Molecular level
Genomics
Sequence level
Species level
Required are:
exact definitions of the
hierarchical levels
the inclusion of optional levels
models for alternative hierarchies
TRANSTax
Taxonomy database of
the biological species
Cell type B
BUDDY
Cell type C
Cell type A
Definition of Gene Expression Matrices
in a Multidimensional Space
Factors controlling
transcription:
TRANSFAC
Spatio-temporal
coordinates:
CYTOMER
Conditional determinants:
TRANSPATH
Cellular level
Cell A Cell B
cytoplasm
nucleus
Cellular level
Cell A Application
Application relevance:
relevance: Cell B
Modeling
Modelingof
ofcell
cellspecificities
specificities(positive
(positiveor
ornegative)
negative)
for
forgene
geneexpression
expressionpatterning
patterning//profiling
profiling
(proteomics
(proteomicsprojects)
projects)
Identification
Identificationand
andmodeling
modelingof
ofthe
themechanisms
mechanisms
of
ofaction
actionof
ofhormones,
hormones,growth
growthfactors,
factors,cytokines
cytokinesetc.
etc.
Cellular level
Additional databases with similar focus:
The Glandular Organ Development Database
http://www.ana.ed.ac.uk/anatomy/database/orghome.html
in here are:
The Kidney Development Database
Early Development of the Lung
Mammary Gland Development Database
Pancreatic Branching Morphogenesis Database
Prostate Gland Branching Morphogenesis Database
The Salivary Gland Development Database
Hierarchical representation
of anatomical
(sub)structures in the Organ
table of CYTOMER
Molecular level
cytoplasm
nucleus
Molecular level
Application
Application relevance:
relevance:
Diagnostic
Diagnosticvalue:
value:Signal
Signaltransduction
transductioncomponents
components
cytoplasm are
areeasily
easilyassayed
assayed
Signal
Signaltransduction
transductioncomponents
componentsare
areexcellent
excellent
candidates
candidatesasastargets
targetsfor
fordrug
drugdesign
design
In
Inconnection
connectionwith
withtranscriptional
transcriptionalregulation:
regulation:
nucleus Key to model intracellular regulatory networks
Key to model intracellular regulatory networks
Database TRANSPATH
http://transfac.gbf.de:8080/TRANSPATH/
Sequence level
Sequence level
Application
Application relevance:
relevance:
Aberrant
Aberranttranscriptional
transcriptionalregulation
regulationis
iscausally
causally
involved
involvedin
innumerous
numerousdiseases,
diseases,e.e.g.
g.cancer,
cancer,
thalassemias,
thalassemias,hemophilia
hemophilia
Precise
Precisetranscriptional
transcriptionalcontrol
controlis
isaaprerequisite
prerequisite
for
forsuccessful
successfulgene
genetherapy
therapyand
andgenetic
genetic
engineering
engineering
Promoter
Promoteranalysis
analysisisisimportant
importantfor
forthe
the
identification
identificationof
oftarget
targetgenes
genes
Sequence level
gene, species / tissue protein interacting region method sequence motif factor bound ref.
gene product
AdMLP adenovirus / HeLa -68 to –49 1a, 3, 4a, 4b TGTAGGCCACGTGACCGG UEF, USF, MLTF 5-10
-63 to –52 1b GGCCACGTGACC USF 9
-40 to +35 1a TATAAAA TFIID 9
....
c-fos human/mouse (3T3) around -346 3, 4b CAGTTCCCGTCAATC SCM-ind. f. 40
/HeLa -320 to -299 (SRE) 1a, 3, 4a, 4b GATGTCCatattaGGACATC SRF 2, 42
mouse/fibr.;B cells -313 to –297 3, 4b GATGTCCatATtaGGACATC „factor 1“ 44
(3T3;WEHI 231)
....
vitellogenin II chicken/oviduct -620 to -597 1a GCGTGACCGGAGCTGAAAGAACAC ER 173, 174
Database TRANSFAC
http://transfac.gbf.de/TRANSFAC/
The Three Ontologies of GO
•Molecular Function — elemental activity or task
nuclease, DNA binding, transcription factor